2008

May 31, 2008

General / Welcome to the New Blog

JB

Welcome to the new blog!  I am currently working on getting an RSS feed up and running soon, and comments enabled again.  I hope you like the new look and the new content as we get it posted.  I’m still working on a better title –
when I get comments working you can post suggestions below!

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June 26, 2008

Biological Change / Evolutionary Theories

JB

Many people are not aware of the many approaches to evolutionary theory taken today.  So I thought I’d summarize several of them, and then comment on their use within Creation biology.  Note that these are not necessarily mutually exclusive, though people tend to focus on the one they think is the most dominant and descriptive of life on earth.

Darwinism / Evolution by natural selection – this is the idea that evolution proceeds (1) by material means only (no planning ahead, no intelligence either in nature or outside of it, except as describable by physical laws), and (2) by historical contingency – the universe doesn’t favor certain possibilties, instead life is almost entirely built out of historical accidents – both the production of a feature through mutation and the mutation’s relevancy within an environment are both essentially accidental.  Traits are propogated by keeping the animal from dying better than other traits.

Platonic Evolution / Structuralism – this is the idea that the laws of nature force biology into certain predefined patterns.  While there is some amount of contingency involved in the production of an organism’s features, the end-products of evolution are based more on physics than on contingency.  A good description of this is in the title of Michael Denton’s book: Nature’s Destiny: How the Laws of Biology Reveal Purpose in the Universe.

Evolution by Symbiogenesis – this is the idea that evolutionary novelty is primarily the result of symbiotic relationships between organisms.  Lynn Margulis’s book, Symbiotic Planet, is a great description of this view of the world.  So, as organisms establish new symbioses, they change their form and functioning within the biosphere.

Front-Loaded Evolution – this is the idea that organisms were created with an initial toolkit, which has elements which can be deployed as needed to survive in new environments.  Different views of this vary as to how fully-formed the toolkit is – i.e. does it have the entire set of information to make a whole structure, or just enough components and pieces that it can arrange them quickly into something workable.  I believe Michael Behe endorses this view.  The website Telic Thoughts is the primary source of advocacy for this opinion. The person pseudonymously known as MikeGene is the primary public mover for this view, and he has a book out called The Design Matrix.

Somatic Selection – This one is not very popular at all, but I’m including it simply because I find the idea fascinating and think it has more merit than it is given credit for.  This is the idea that evolution actually occurs in body cells first, and then successful combinations found in the body cells get transferred via reverse transcription to reproductive cells.  The primary work espousing this view is Lamarck’s Signature.

The interesting thing is that, as theories of evolution, none of these is explicitly against Creationism.  Biblically, the mechanism of diversification from the original kinds is not specified, and therefore, any of them are compatible biblicallly.  Scientifically, I don’t think Darwinism makes much sense, but, as a view of biological change, is not strictly anti-biblical.

Now, where most evolutionary theories do go against Biblical Creation is in:

  • Being tied to old-earth assumptions
  • Being tied to the assumptions of universal or near-universal common ancestry
  • Being used as an explanation for the origins of life 

Anyway, the point of all this is as follows:

  • Evolution is not a monolithic entity.  A lot of people view the debate is about “creation” verses “evolution”, as if they were necessarily distinct in all facets, and as if they were discreet entities.  Evolution is not a single thing, and, at least as the mechanism of diversification goes, neither is Creation.
  • When someone says “evolution is proven” it would help if it was specified which evolution was proven and for what parameters 🙂
  • While the evolutionary biological literature should not be taken as gospel, there is no reason to discount many of the mechanisms out-of-hand even if we disagree with how they may be applied.

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June 25, 2008

Information Theory / Enabling Conditions for Open-Ended Evolution

JB

I just finished reading Enabling Conditions for ‘Open-Ended Evolution’.  In a word – fantastic.

These three put together the best summary of a defence for a designed origin of life as I’ve seen.  Of course, they didn’t say that – they couched everything in evolutionary terms.  Nonetheless, I would recommend it for anyone’s reading.

My one major critique is that they seem to be focused on the idea of “open-ended evolution”.  While I agree that the conditions that they list would be necessary conditions for life to meet in order for open-ended evolution to occur, I disagree that truly open-ended evolution could occur, at least as they have defined it.  Specifically, one of the definitions they seem to agree with for this term says:

Also, by using the term ‘open-ended’ I wish to imply that an indefinite variety of phenotypes are attainable through the evolutionary process, rather than continuous change being achieved by, for example, cycling through a finite set of possible forms.

I’m not sure if I would argue that my own view is that the set is necessarily finite, but that it is necessarily bounded by some properties rather than open-ended.

Anyway, the case they argued was this:

  • In order for a complex metabolic network to be sustainable (i.e. exist as a proto-organism), it must be cyclic 
  • In order for that network to be reproduceable, it has to have a way of encoding relevant information about the network in a way that is:
    • Copyable
    • Readable
    • Sequenceable (i.e. the information must be able to sequence complex interactions)
  • The same chemical system cannot be used to store information and perform metabolic activity, because:
    • The chemical composition of the information must be relatively inert, in order to be able to encode arbitrary configurations of metabolic networks
    • The chemical composition of the metabolic network must not be inert, in order to perform the tasks of metabolism
    • The information must be readable/copyable, which implies a 3D configuration optimized for reading
    • The metabolic network must function, which implies a 3D configuration optimized for engaging in dynamic behavior with the environment
    • Evolutionarily, changes in the “information” part of the system to encode new functions cannot interfere with the existing metabolic network, or it would fall apart during evolution (changing the sequences would cause the information itself to change its own role as an active player – so it wouldn’t code for information, but rather be an active component).
  • The metabolic network, in order to read the information to reconstruct itself, must be under formal constraints instead of physical constraints (i.e. it has to obey an established formal rule of interpretation in order to use the information) — “At the roots of this coupling between endergonic and exergonic processes there must be
    the capacity of a chemical system to build and rebuild (maintain) by itself a diverse set of boundary conditions, or ‘constraints’. We do not refer here to the standard (typically structural and external) constraints that help to solve a dynamical problem in physics, by reducing the degrees of freedom of a system; but to self-generated constraints (new ‘highlevel rules’ that affect ‘low-level molecular interactions’) coming both from self-assembly and self-organization phenomena“

So, while using the language of self-assembly, self-organization, RNA world, etc., the authors were able to show why life is a holistic unit, unexplainable in a reductionistic manne, and certainly not by the mechanisms mentioned.

In fact, it is amusing – each stage that was mentioned was shown to be incapable of open-ended evolution, yet the paper, with some magic words, was able to transition us to the next “stage”, despite the fact that the author had just said that the previous stage was not open to open-ended evolution!

Anyway, it was a great paper.  Creation researches should pay special attention tothe separation of the metabolism from the information and why that is important.  Also, I thought that it was an excellent description of a non-reductable (i.e. irreducibly complex) system, with explicit functional/theoretical reasons (not just complexity) as to why all parts of the system are needed at once.

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June 05, 2008

Biological Change / Another Interesting Perspective on Podarcis sicula

JB

Physorg pointed out another interesting perspective on the new organ within the lizards:

“Cecal valve evolution probably went hand-in-hand with a novel association between the lizards on Pod Mrcaru and microorganisms called nematodes that break down cellulose, which were found in their hindguts”

We have talked about symbiosis as a cause of biological diversity and speciation before.  Here, it could be that a symbiosis actually induced a “new” (to the population) organ to develop.

Very interesting! 

In the first of the above two links, Joe Francis talks about the immune system potentially being a part of detecting and picking up symbiotic partners.  It would be interesting to know if that is how the symbiotic association began, and if that is also what facilitated the growing of the cecal valve. 

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June 05, 2008

Biological Change / Rapid Adaptation in Podarcis sicula

JB

I have been planning on writing on this very exciting paper, but Jean Lightner beat me to it 🙂

In 36 years, a group of lizards which were separated onto a different island from the rest of their species had:

  • Changed their head size
  • Changed their diet to be much more plant-heavy
  • Developed a new (not present in the parent population) organ – the cecal valve – to help digest the more plant-heavy diet
  • Developed new symbiotic relationships
  • Changed their behavior

In case you didn’t notice the bolding, it was the development of the new organ that I found most interesting.  Now, when I say “new”, that just means new to them.  The cecal valve is present in a number of species.  However, it was not present in the population which the island was seeded with. 

This gives a lot of creedence to the front-loaded “toolbox” concept of Intelligent Design.  That is, species have an available set of rapidly-deployable changes which can be induced as needed.  Many parts of this toolbox are shared by many related and non-related organisms.

The fact that in only 36 years all of these changes happened indicate that it was part of a built-in process. 

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June 01, 2008

Discussions around the Web / Design Constraints for Building Materials

JB

TelicThoughts has a very interesting discussion on what the requirements of building materials might be for designing life.  Check it out – very interesting discussion!  I don’t think many of them understood my arguments relating to complexity theory.  I hope to expound some of those out in a more extended manner soon.

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July 29, 2008

General / Schedule for BSG Posted

JB

The schedule for the BSG conference has been posted.  As you can see, I’ll be talking about what Wolfram’s complexity classes can tell us about Irreducible Complexity.  I’m sure that Stephen Wolfram would cringe if he knew that’s what his research was being used for.  That makes me both happy and sad – happy because it was somewhat providential that I came to know about A New Kind of Science, and sad because I wish that I could repay Stephen for the good he and his company has done my family, and I don’t think that he would take too kindly to the direction that I’m taking his work.

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July 27, 2008

Information Theory / Metaprogramming as a model for VDJ Rearrangements

JB

Two years ago I gave a talk to the BSG on how the genome acts as a metaprogramming system during VDJ recombination (see R14).  I was wanting to get someone to do additional testing on this, or at least write it up as a proper paper before presenting it on the blog, but since I haven’t had the time or resources for either, I figure I’ll just go ahead and post it.

A Quick Introduction to Metaprogramming

All computer programmers are inherently lazy – that’s why the only thing we are good at is getting computers to do things for us.  In fact, we’re so lazy, if we can write a program for the computer to generate code for us, we will.  Such programs – programs to generate programs – are called metaprograms.  If you’re interested in the computer programming aspect of metaprograms, I wrote three-part tutorial series on it (Part 1 | Part 2 | Part 3).

But the key parts of metaprogramming are these:

  • The programmer specifies solutions in a domain-specific manner – that is, in a format that is specialized to the task at hand
  • The metaprogramming system then rearranges, rewrites, and otherwise remakes the domain-specific program into a program in the standard language which is to be translated
  • The metaprogramming system is responsible for making the parts of the metaprogram interact correctly

Metaprogramming systems are used to abstract away two things that make programming difficult:

  • Redundant specifications
  • Interaction issues between pieces
  • Mismatches between the problem domain and the solution domain

Now, because metaprogramming systems are doing all of this, it necessarily means that metaprogramming systems are narrow in scope.

A Quick Introduction to V(D)J Recombination

The cell can generate millions or billions of antibodies out of a relatively few number of genes.  It does this by splitting antibodies into four regions – the variable region (V), the diversity region (D), the joining region (J), and the constant region (C).  Each of these regions has multiple genes associated with it, separated by Recombination Signal Sequences (RSSs) and spacers.  Heavy chain antibodies use all four types of regions, while light-chain antibodies just use V, J, and C regions.  The constant regions are (surprise!) constant within an antibody class.

So, when B-cells mature, they pick a single gene from each of the V, D, and J regions, assemble them together, and join them to the constant region of the antibody.  The VDJ regions specify the affinity of the gene towards an antigen (which is why it needs so much diversity), while the C region specifies the attachment to the cell (which is why it remains constant).  

However, when VDJ regions are recombined, an interesting thing happens – a series of non-templated (N) and/or Palindromic (P) elements are inserted between these regions.   Current efforts so far (as of the 2006 paper – I haven’t kept up since then) have classified these as “random” insertions.  What can the Creation model offer?

Note –This paper is a good starting point if you want to know more about V(D)J Recombination in general.

V(D)J Recombination as a Metaprogramming System

So, in V(D)J recombination, you have

  • A series of code rearrangements
  • V, D, and J segments all being pulled from a bucket of similar genes and stitched together
  • The whole thing being attached to a constant region
  • All of these parts contributing to a narrow biological focus
  • The rearrangement system is adding in non-templated code in-between the joined-together segments

So, in the metaprogramming model, what is the role of the rearranging system?  It is to not only help the parts of the code go into their correct places and add-in the non-redundant parts, but to also manage the interactions of the parts, so that the recombine properly.

Therefore, if V(D)J recombination is acting as a metaprogramming system, then the probable reason for the addition of N and P elements is to manage the interaction of the parts.  This lets the V, D, and J components evolve more freely without having to worry about how they will interact with the other parts of the recombination system.  The recombination system worries about how the parts will interact.

So, is there any evidence that this is what is going on?  Actually there is.  In certain mouse antibodies, arginine is required at position 96 in order for the antibody to have proper affinity.  Interestingly, this was always generated during recombination in the cases where it was required, even if it wasn’t coded for by either of the joined segments!  It appears as though the V(D)J recombination system knows that the arginine is required for affinity, and therefore is able to generate it when necessary.

Now, there are two possible pieces of counter-evidence which I am aware of:

  • Some antibodies recombine in multiple ways using the same template pieces. 
  • Some recombinations are in fact unproductive

However, the first one could simply be because either (a) the recombination system is directional but non-deterministic (i.e. it biases outcomes that are probably workable, but doesn’t limit the outcome to a single possibility), or (b) there are additional elements at play, (c) both (a) and (b).

The second one could be the result of a non-deterministic system – that it only biases good results but doesn’t guarantee them.

Obviously, this needs experimenting before it is taken as fact, but I think the evidence currently points in this direction.

Other Metaprogramming Possibilities

If the V(D)J recombination system is actually a metaprogramming system, there are some other possibilities worth looking into:

  • There is currently an “unused” region of nucleotides that is a “spacer” between the RSS and the unrecombined genes.  Could that possibly contain metadata about the frequencies and occasions which that gene should be used?
  • Non-homologous end-joining uses a similar recombination method to V(D)J recombination.  Perhaps it also contains heuristics about how the affinities of genes works and how they can be recombined.

Enterprise Metaprogramming and Biology

The V(D)J Recombination system is a fairly standard metaprogramming system.  However, in Computer Science we have another type of metaprogramming facility, called an “enterprise” metaprogram.  In these, the specifications are actually specifications for multiple different subsystems.  That is, a single template is run through multiple metaprogramming systems (one for each subsystem), and it can generate a unified, interacting system.

So, in biology, we would be looking for a system that recombined one way in one tissue, and recombined another way in another tissue, in such a way that variations in those genes would cause the two tissue types to change in coordination with each other.  Alternatively, we might be more likely to find, instead of a recombination system, a mechanism of alternative splicing, so that one gene is spliced in different ways, depending on the tissue, but spliced in such a way that changes within the gene through evolution would cause coordinating changes in the protein products in multiple tissues.  

NOTE – there are several claims here that are unreferenced.  If you are interested in them, mention it in the comments, and I will try to look it up for you.  As I said, it’s been two years since I did this research, and it’s been pretty much sitting on a shelf since then, so it may take me a few days to find.

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July 09, 2008

General / Convergent Evolution – the Platypus

JB

I found this awfully funny.

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July 07, 2008

General / ICC and BSG Conference Schedules Online

JB

The schedule to this year’s Creation Biology Study Group meeting was just posted.  Register by July 11th to get the early bird discount!

Also, the International Conference on Creationism also has their schedule posted.

Note that both conferences are in the same location on the same week.  ICC is on the first half of the week, and BSG is on the second half.

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July 02, 2008

Dinosaurs / Dinosaurs, John Calvin, and Papua New Guinea

JB

Many creationists hold various opinions about whether or not Dinosaurs lived very far past the flood.  Some think they were not on the ark, some think they died out immediately after, some think they lived until the middle ages, and some think that a few of them are still hanging around today.  I used to be bullish for the idea of present-day dinosaurs, but I’ve become slightly more skeptical.  However, I still think it is an idea meriting discussions.

Today, I found in Google reader two interesting stories about modern or semi-modern Dinosaurs, one from CMI and one from AiG:

Anyway, I always find new Dinosaur stuff interesting.

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August 29, 2008

Biological Change / The Production of Variability in Spiders

JB

For those interested, I did a follow-up post about the production of variations in spiders over at UncommonDescent.  The original conversation about the production of variability is here.

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August 29, 2008

General / 63rd Annual ASA Meeting

JB

For those interested, a podcast of the 63rd ASA meeting is now available on iTunes.  HT to The Creation of an Evolutionist for pointing this out.  The ASA is mainly a theistic evolutionary crowd, but that doesn’t mean they don’t have good things to say.  If nothing else, it is good to know what those who disagree with you actually think in their strongest forms, rather than just passing around straw-man versions of those positions among people who already agree with you.

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August 27, 2008

Information Theory / Mathematics Points to Design

JB

Progetto Cosmo has a fantastic article which deals with some of the interesting problems that have been encountered in the last century in mathematics, and how those problems relate to intelligence and design. 

They document the progress of work in Godel, Chaitin, von Neumann, and others, and show how each of them came to the conclusion that, fundamentally in life (not just biology), more does not come from less.  It is a great tour of some of the thinking that is fundamental to design yet is often times ignored in sound-bite debates.

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August 26, 2008

Discussions around the Web / MicroRNAs and Design

JB

UncommonDescent has a fascinating discussion about the design implications of MicroRNAs. The importance is stated by DaveScot in the comments:

Each specific base pair sequence of length n [i.e. the MicroRNA targets], has a probability of 1/n^4. An 8 pair sequence has a pobability of 1/4^8 or ~ 1/64000. To have two that match I think we need to multiply the probabilities of each. Get the drift? After seeing the same target sequence not a couple but hundreds of times, and in the protein target groups that give the right combinations for function, doesn’t design spring to your mind?

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August 23, 2008

Discussions around the Web / End of August Discussions and Links

JB

There is almost too much going on these days to keep up with!  I’ll try to let you in on some of the craziness:

Front-loading

A lot of people have been discussing front-loading.  Here’s some of the links:

New Blogs I’m Watching

I’ve found several blogs.  These two appear to be very interesting indeed:

Other Stuff

If I blogged on all that stuff, I’d never sleep!  Hope some of it interests you.

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August 21, 2008

Geology / The Late Appearance of Humans in the Fossil Record

JB

Currently in Creationism there are two puzzling issues with regards to the fossil record:

  • Where are the mammals in the flood sediments?
  • Where are the humans in the post-flood sediments?

The fossil record of the flood strata is fairly easy to understand if we look at it as consecutive habitats which get washed away.  The one big problem with this theory is that there is an entire biome (the mammals) that appears to be missing.  There have been many possibilities considered for this one, including:

  • The population of mammals pre-flood was small enough to not be well-represented in flood sediments
  • The mammalian biome was subducted into the earth during the flood
  • Probably others I can’t think of right now

Sadly, this is not actually the topic of this post, I just thought I’d throw it in for free 🙂

After the flood (if you view the end of the flood as the K/T boundary), the fossil record is fairly consistent with the idea of a post-flood repopulation of the earth.  The marsupials seem to be the fastest to get anywhere, with the placentals being slower but more dominating.

So why are the apes consistently before humans in the fossil record?  Kurt Wise’s take on this – it’s because of Babel.   After the flood the animals were obedient – they spread out and repopulated the earth.  The humans, however, were not obedient.  They stayed in the same spot at Babel.  This caused the animals to have a very large head-start in repopulating the earth, which is one of the reasons why apes always precede humans in the fossil record, and why the humans appear to be the only baramin whose fossil record does not extend back to the flood.

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August 20, 2008

General / Around the Web – Flagellar Assembly Video, Book on Origins, and Galileo

JB

Osaka University has some really great stuff on the bacterial flagellum:

 I also found a book online called Origins and Destiny: A Scientist Examines God’s Handiwork.  It’s not fantastic, but it is decent.  I was actually searching for some of his other work and had no idea that he had this book, nor that it was online for free.  Anway, take a look at it if you’re interested.

Some new research has given us another possible reason for Galileo’s trial – basically that the Tuscan Duke of Medici refused to aid Rome in its war efforts against France, and so Pope Urban VIII punished the Duke by arresting Galileo, who was the Duke’s personal friend.  So why is this theory plausible?  It is the reason given in the first biography of Galileo – only 20 years after his death.

What’s really good to know is that the science-vs-religion aspect is no longer in vogue among scholars:

Not that modern scholars give much credence to the traditional science-vs.-religion interpretation of the trial. Most Galilean researchers today agree that politics played a much bigger role than religious closed-mindedness, but there is spirited disagreement about the specifics. Some think the pope was angry at being parodied by Galileo’s character Simplicius in Dialogue Concerning the Two Chief World Systems­. Other scholars have suggested that church leaders felt Galileo had tricked them into granting him a license to write the book by not revealing its Copernican leanings. But “Salusbury’s explanation is kind of refreshingly new,” Wilding says.

So now, at the very least, we have agreement that even Galileo’s own contemporaries did not view the trial as being science-vs-religion, but rather more of a political problem.

I also found another book for free online that I will never have time to read – The Computational Beauty of Nature. 

Note to self – need to read The Onset of Selection (sorry – this blog is better-catalogued than my bookmarks on my browser)

Random questions for my readers:

  • What’s your favorite symbiosis?
  • What’s your favorite instance of convergent evolution? 

Hope you are sleeping better than I am!

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August 18, 2008

Biological Change / The Production of Variability

JB

Most people don’t understand the problems of the production of variability in biology (or actually in any complex system), and especially how it relates to Intelligent Design.  Here are some links to my current work on the subject:

UPDATE – followup blog entry – applying some of these concepts to spiders

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August 16, 2008

Natural Evil / It’s Rough Being a Sea Monkey

Several of our friends at Bryan College are working on problems about natural evil – how did predation come about in a world that was supposed to be “very good”?  Currently, they are looking at nematocysts as killing machines – delivering toxins that stun or kill the victim.

One thought was that the nematocysts were originally less toxic – perhaps delivering something less than a killing blow.  One thought was that perhaps symbiotic relationships might affect the toxicity of the sting.  As a model system, the Bryan College team began by studying the feeding habits of green hydra, who use nematocysts to stun and kill their prey before eating them.  They were fed Sea Monkeys (Artemia) and their feeding patterns were observed.  Unfortunately, the toxins were too toxic to the Artemia to be of use in toxicity assays, but they managed to garner some cool Hydra feeding videos in the process.  All of the videos are sped up in order to make it a little more exciting.  However, for a true-speed video, here is a Hydra swallow in real-time.

Anyway, many thanks to the BryanCORE guys for lending me the videos!  For more information, you can read the research abstract (it is abstract C2).

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August 14, 2008

General / Creation/Evolution Literature Database

JB

Bryan Center for Origins Research announced at the BSG conference the availability of the new CELD database for searching through Creation-oriented literature and abstracts.  Think of it as kind of like Pubmed for Creationists.  I believe it goes back to the 1800s for some of the indexed journals.  They have their full journal list available.

Anyway, happy searching!

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October 31, 2008

General / Catholic Creationism Conference This Weekend

I doubt that many of you will be in Rome next week, but I still thought you might be interested to know about the Catholic Creationism conference being held there next week.  The topics covered are pretty basic, but it is good to see elements of the Catholic church supporting Creationism.

Now, of course, they actually don’t call themselves Creationists:

The scientists participating in the conference at Sapienza University are not creationists. They represent thousands of world-renowned scientists whose evidence against evolution is often downplayed or ignored by academics who support evolution.

But I know that Berthault is a diluvialist at least.  However, Berthault doesn’t consider himself a Creationist because his position is based on data, not theology.

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October 22, 2008

General / The Changing Understanding of Pseudogenes

JB

Our understanding of pseudogenes is currently being revolutionized.  Jean Lightner reviews some literature which discusses pseudogenes that code for proteins!  Pseudogenes have already been shown to provide lots of different types of regulation, but now we are seeing that different ways of reading the genes can actually produce functioning proteins from pseudogenes.

This should re-emphasize a point – science is always changing.  Those of you who think that we should put our faith in science instead of God and God’s word in scripture, remember that what we think we know today about science can turn out wrong tomorrow.  Science is great, but only if we understand it as a subordinate discipline.  Science is a servant, not a master.  Many of the “proofs” of evolution are based off of things that we are only beginning to understand. 

I worry that the Church is banking too much on the “established fact” of evolution.  There is so much theology that is currently being systematically skewed because even conservative evangelicals are shifting to the evolutionary paradigm.

Matthew 24:24 – “For false Christs and false prophets will arise and will show great signs and wonders, so as to mislead, if possible, even the elect.”

I think many Christians are turning to science as a false Christ and false prophet.  If you look at the way they justify their theology, it is based on all of the wonderful achievements of science, and then they go and reinterpret the whole Bible based on an evolutionary paradigm.  That rings to me of following a false Christ because of signs and wonders.

2 Peter 3:3-6 – “First of all, you must understand that in the last days scoffers will come, scoffing and following their own evil desires. They will say, “Where is this ‘coming’ he promised? Ever since our fathers died, everything goes on as it has since the beginning of creation.” 5But they deliberately forget that long ago by God’s word the heavens existed and the earth was formed out of water and by water. 6By these waters also the world of that time was deluged and destroyed.”

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October 21, 2008

General / Intellectual Honesty

JB

MikeGene has had several great posts of late but I haven’t had time to blog on them.  However this one I think is important enough for us that I’m taking the time to post it: 10 Signs of Intellectual Honesty.  This is a very easy value to sacrifice when trying to convince people of the value of your position, especially when something important like scripture or creation is being discussed.  However, I would argue that overreaching/intellectual dishonesty have the biggest long-term downsides.

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October 21, 2008

Discussions around the Web / Ken Ham on BeliefNet

JB

Apparently Ken Ham will be appearing on a web debate among Christians on BeliefNet, debating Karl Giberson.  Could be interesting, annoying, or painful.  We’ll see.  I’m currently reading Nature’s Witness: How Evolution Can Inspire Faith.  Afterwards, I’ll review it, with an eye towards why I think Creationism is important to the Church.  Maybe Ken and I can compare answers afterwards 🙂

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October 12, 2008

General / New animal discovered 1.74 miles below surface

JB

This looks very cool.

D. audaxviator survives in a habitat where it gets its energy not from the sun but from hydrogen and sulfate produced by the radioactive decay of uranium.

The original article has a picture – this is a micro-organism that was collected from cave-water.

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October 05, 2008

Physics and Cosmology / Plasma Universe

JB

It seems like all of the research in YEC is going towards cosmology physics.  Some reasons why this might be are:

  • Physics departments have less resentment towards Creationists than do biology departments
  • Showing the reasonableness of the Creationist timeline does a double-whammy by also removing evolutionary timescales
  • It’s just plain interesting, with a lot of work available to do

Anyway, as usual, I know next to nothing about physics, and I promise to try to educate myself on this sometime before global warming switches back to global cooling.

Barry Setterfield is an interesting character in YEC.  Here’s his latest paper reviewing the potential for the Universe to have a primarily plasma origin.  If I remember correctly, Setterfield believes that the “formless and void” state of the universe in Genesis was a plasma of hydrogen and oxygen.  I have no idea if that relates to the paper or not 🙂  As I said, someday…

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October 03, 2008

Discussions around the Web / Ian Juby’s New Website

JB

For those of you interested, Ian Juby just overhauled his website, and has some interesting material on it.  Ian has regularly allowed me to repost his emails and newsletters here which have had some pretty interesting material in it.  For instance, Ian reported on the cause of “death pose” in dinosaurs long before it was published in technical journals.

He also is starting a new blog which I will suggest for those of you wanting to keep current.

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October 01, 2008

General / Caterpillars – Cute and Stinging

JB

My wife found a cool-looking caterpillar outside near the sandbox.  Turns out it is potentially a stinging caterpillar.  Anyway, we are keeping it for a pet in a butterfly cage.  It is a Banded Tussock Moth (Halysidota tessellaris).

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November 30, 2008

Geology / Russ Humphreys Latest Summary of Helium Work

JB

Russ Humphreys just published a summary of the current debate regarding his Helium dating methods, complete with an index of criticisms and responses.  Of considerable interested is figure 3, which graphs his predicted data based on a young earth, compared to the predicted data for an old earth, compared to experimental values.

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November 29, 2008

Biological Change / A Catalogue of Animal and Plant Baramins (Created Kinds)

JB

Todd Wood just release a new monograph containing a whole bunch of data concerning created kinds, called Animal and Plant Baramins.  For those of you new to Creationism, a baramin is the Creationist term for a “created kind”.  For those interested in exploring Creation systematics further, I will refer you to Wood and Wise’s  A Refined Baramin Concept.

Anyway, this book is significant because it is the first large-scale treatment of what organisms belong with which created kind (again, for those who are new, Creationists believe that Created Kinds are larger than just “species”, and usually estimate the Created Kind to be roughly equivalent with the family level of taxonomy).

Now, I have no first-hand information about the book – it just came out so I haven’t read any of it yet, but I did talk with Todd about it at this year’s BSG.  Based on that conversation, I’m pretty sure that most baramins in the book are defined using statistical baraminic concepts.  I’m not a big fan of statistical baraminology, and prefer hybridization experiments (obviously, however, that data is not available for fossil species).  In any case, this is a great start to our systematics work. 

Another thing that Todd told me is that ark-based animals have much less variability within baramins than non-ark-based animals.  This is quite interesting, since the ark-based animals would have a genetic bottleneck that wouldn’t apply to non-ark-based animals.  I believe he also said that the distribution actually follows what would be expected from a Biblical timescale.

Anyway, I plan on purchasing this as soon as I have the funds, and for those into Creation systematics, I would suggest you do, too.

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November 28, 2008

Geology / Marine Fossils Preserved in Amber

JB

“New Discoveries” has a writeup of a new PNAS paper, Evidence for marine microfossils from amber.  Remember, amber comes from tree sap, and marine microfossils come from the sea 🙂  Although the paper was not speaking of the Biblical Flood, New Discoveries quoted the following from their pages to explain their findings:

It is likely that the flood waters first broke trees apart, transported the shattered timber, and then deposited the remaining pieces. These would have extruded large quantities of sap, which would have engulfed nearby creatures and then, at the bottom of the flood waters, hardened into amber. Marine algae trapped in amber ought to finally prove a flood-based interpretation.

I don’t have access to the paper at the moment, but this seemed really interesting.

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November 26, 2008

Information Theory / Optimality of the Genetic Code

JB

Teleomechanist has a great post up with a literature review about the optimality of the genetic code.

The genetic code seems to be designed with the following features:

  • Error minimization in protein construction on simple genetic mutations
  • Minimizing bad effects of frameshift errors
  • Error detection/correction through parity checking
  • Ability to layer on additional codes (the original paper for this is worthwhile) to the protein sequence

Anyway, Teleomachinist lists a lot of other interesting aspects about the genetic code, but I thought these were the top ones.  I especially like the fact that the genome seems to be optimized for having additional codes layered on.  That is very interesting indeed.

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November 26, 2008

General / Creation Research Society Conference

JB

The Creation Research Society is sponsoring a conference this summer at the University of South Carolina Lancaster.  I think this is CRS’s first conference.  Anyone can attend, but you have to be a voting member of CRS to author a paper (or have a voting member as a co-author).

Anyway, I’m probably going to be at the BSG conference this year, though at the moment it does not appear that I will have anything myself to present.  Come to think of it, that might actually make it more fun.

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November 23, 2008

General / A Short History of Creationism

JB

While the whole book is pretty long, if anyone wants a short introduction to the history of Creationism, I would suggest reading the last chapter of Ronald Numbers’ The Creationists.  I’m actually reading an older edition, so if it has changed the chapter is called “Creation Science Floods the World”.  Anyway, it was a very good, short, history of the worldwide movement.

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November 20, 2008

General / BSG Newsletter and an Opportunity for Students to Get Involved

JB

The Creation Biology Study Group is working on putting out a newsletter a few times throughout the year.  It will consist of book reviews, literature commentaries, and question/answer sections.  For those of you who are interested in Creation Research, but don’t know where to start or how to get involved, consider contributing to the newsletter!  To contribute to the newsletter or to read the newsletter you will have to be a member of the Creation Biology Study Group.  Also, we are having a question/answer section where students can ask questions and have them answered, so feel free to ask!  Again, this is a great way to start contributing to Creation research.

Here is the full announcement:

————–

Fellow BSG Members

We are looking to put together our first ever BSG newsletter.  This is going to be primarily member-contributed material, so please read on and see what you can do to help!  If you are a student, and want to start being active in Creation biology – this is a good way to get started!  The details and schedule for contributions are at the bottom of the email.  All newsletter-related email should be sent to bsg@bartlettpublishing.com .  The newsletter has two main goals:

1) Continue studying God’s creation together
2) Encourage new participants and students to join in who might not be able to make it to the conferences

So, here’s how I plan to organize the newsletter:

1) Book Reviews by BSG Members
2) Literature Commentaries by BSG Members
3) Current Happenings in the BSG Community
4) Creation Biology Questions and Answers
5) Member Correspondence

1) Book Reviews

The book reviews will be reviews of both creationary and non-creationary books.  The goal is the critical evaluation of books in terms of accuracy of the science, history, or philosophy presented.  Reviews of evolution-oriented books should point out items of value to our research goals and must not attack such books using anti-evolution polemics.  Likewise, reviews that favorably present creation-oriented books without critical evaluation of the content are not acceptable.   It is my hope this feature will encourage  wider reading of scholarly books so the BSG members will be well versed in both creationary and evolutionary current thinking.

Book reviews can be submitted by anyone, and if you are a student this is probably a good area to help out in.  There are no minimum or maximum lengths.  If you aren’t sure how to start or what to review, just send us an email and we’ll hook you up.

To get an idea of what we are looking for, here are some suggested books to look at (please don’t feel limited by these!):

The Design Matrix: A Consilience of Clues
Evolution through Genetic Exchange
Evolution and the Levels of Selection
Science and Grace: God’s Reign in the Natural Sciences
The Biology of Coastal Sand Dunes
Polar Lakes and Rivers: Limnology of Arctic and Antarctic Aquatic Ecosystems
Chance in Biology: Using Probability to Explore Nature
A Creationist Review and Preliminary Analysis of the History, Geology, Climate and Biology of the Galapágos Islands.
How and Why Species Multiply: The Radiation of Darwin’s Finches
Ecological Stoichiometry: The Biology of Elements from Molecules to the Biosphere
Cornell Lab of Ornithology Handbook of Bird Biology
Foundations of Systems Biology
The Biotic Message
The Regulatory Genome: Gene Regulatory Networks in Development and Evolution
Evolutionary Dynamics: Exploring the Equations of Life
The Structure and Dynamics of Networks
The Genesis Factor: Myths and Realities
2) Literature Commentaries

Literature commentaries can cover any paper, especially conventional papers whose results have application to creation biology.  The commentary should begin with the full citation of the article.  This should be followed by one or two short paragraphs summarizing the article’s findings and one or two short paragraphs suggesting a creation biology application.

3) Current Happenings in the BSG Community

Anything that you think that the BSG Community might be interested in, please let us know!  This includes papers published, conferences happenings, and even personal stuff like job changes, marriages, and babies.  Please note that the newsletter will be semi-private—that is, we will only make it available to BSG members, but that is not a guarantee to privacy.  So please do not submit anything that you wouldn’t want others to see or find out about.

4) Questions and Answers

This is a section where you can ask questions and have them answered by our community. Submit questions to the newletter editor, who will contact an appropriate expert in our community.  The question and answer will be published together. This section can be used for students to get their deepest, darkest questions answered.

Researchers who want feedback on planned projects and ideas should submit to the newsletter editor a brief project proposal along with their e-mail address to be published in the newsletter.   Readers having comments on the proposal can then contact the researcher directly.

5) Members Correspondence

This is a place to comment about anything which occurred in the previous newsletter or in a previous conference.  If you have a note, question, or other correspondence about the happenings of the BSG, this is the place to share them.

SUBMISSION INFORMATION AND DEADLINES

I plan on publishing the newsletter late in January.  Therefore, for book reviews and literature reviews, please email me your topic within the next week.  If you would like to contribute, but need some direction, please email me immediately and we’ll figure something out.  The reviews themselves need to be in by December 31st.  All other material can be submitted until January 15th.  Send all newsletter-related items to bsg@bartlettpublishing.com .

SUBMISSION POLICIES

The newsletter is not a full peer-review process.  All entries will be reviewed by the newsletter editor with final approval by the executive editor.  Copyright for all entries will remain with the submission author.  However, by submitting an entry you are granting the BSG an unlimited, royalty-free license to use your submission.


Literature commentaries can cover any paper, especially conventional papers whose results have application to creation biology.  The commentary should begin with the full citation of the article.  This should be followed by one or two short paragraphs summarizing the article’s findings and one or two short paragraphs suggesting a creation biology application.

3) Current Happenings in the BSG Community

Anything that you think that the BSG Community might be interested in, please let us know!  This includes papers published, conferences happenings, and even personal stuff like job changes, marriages, and babies.  Please note that the newsletter will be semi-private—that is, we will only make it available to BSG members, but that is not a guarantee to privacy.  So please do not submit anything that you wouldn’t want others to see or find out about.

4) Questions and Answers

This is a section where you can ask questions and have them answered by our community. Submit questions to the newletter editor, who will contact an appropriate expert in our community.  The question and answer will be published together. This section can be used for students to get their deepest, darkest questions answered.

Researchers who want feedback on planned projects and ideas should submit to the newsletter editor a brief project proposal along with their e-mail address to be published in the newsletter.   Readers having comments on the proposal can then contact the researcher directly.

5) Members Correspondence

This is a place to comment about anything which occurred in the previous newsletter or in a previous conference.  If you have a note, question, or other correspondence about the happenings of the BSG, this is the place to share them.

SUBMISSION INFORMATION AND DEADLINES

I plan on publishing the newsletter late in January.  Therefore, for book reviews and literature reviews, please email me your topic within the next week.  If you would like to contribute, but need some direction, please email me immediately and we’ll figure something out.  The reviews themselves need to be in by December 31st.  All other material can be submitted until January 15th.  Send all newsletter-related items to bsg@bartlettpublishing.com .

SUBMISSION POLICIES

The newsletter is not a full peer-review process.  All entries will be reviewed by the newsletter editor with final approval by the executive editor.  Copyright for all entries will remain with the submission author.  However, by submitting an entry you are granting the BSG an unlimited, royalty-free license to use your submission.

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November 12, 2008

General / Royal Society Digital Archive Free untile February

JB

For those of you interested in scholarly content, the Royal Society has just announced that it will make its archives available for free to everyone until February 1st, 2009.

The Royal Society is a top publisher of scientific papers, and their archives go back to 1665!  So,  if you are interested in the history of science, this is a perfect place to go searching.

Exciting!

If you find any interesting papers of note, please mention them on the comments.

December 31, 2008

Information Theory / Randomness in Creation Biology

JB

After a year and a half of waiting, my paper on randomness and Creation Biology has finally been published in the current CRSQ!  The paper is titled “Statistical and Philosophical Notions of Chance in Creation Biology”.  The main points of the paper follow:

More Than One Meaning for Random

There are different notions of chance and randomness which have very different implications, but we tend to lump them all together.  This causes sloppy thinking and can blind the way we look at things.  This is true in both Creationary and Evolutionary literature.

One type of randomness is statistical randomness.  A process is statistically random if events in that process occur with fixed percentage frequencies over every “normal” infinite subset of those events.  Another type is philosophical randomness.  A process is philosophically random if it occurs outside the constraints of a system.  The state of a slot machine after pulling its lever is the result of statistical randomness.  The state of a slot machine after being hit by a meteor is the result of philosophical randomness.

Statistical randomness is often used in engineering to great benefit.  It offers a way of counteracting unknowns.  I’ll probably devote a post to statistical randomness at a later date.

Preadaptation

The Luria/Delbrück and Lederberg experiments (which are normally used to prove the randomness of mutations) are not by themselves evidence of an unplanned process.  Another possibility explored in the paper are that many of these are pre-adaptive mechanisms.

Basically, I think that many “spontaneous” mutations are actually the result of a process to increase a population’s future fitness.  Basically, it forces alternate biochemical configurations into the population at a controlled rate, so that a catastrophic environmental change does not wipe out the entire population.  If a cell uses a statistically random process to create these alternate configurations, the population can keep fixed percentages of alternate configurations without any individual cell needing to know how many of each configuration are already in the population.

Therefore, I think that many (but not all) of the “spontaneous” mutations we see are not haphazard just because they occur in the absence of selection, but instead are planned mechanisms to introduce alternate biochemical configurations into the population (which are likely less fit in the current environment) to prepare for extreme changes to the environment in the future.

Testing for Whether Mutational Hot Spots are Planned or Haphazard

Mutational “hot spots” within the genome may be either the result of a planned mutational mechanism or just the happenstance physical interactions of biochemistry.  I proposed that the proper test for this would be whether or not mutations within the hot spot are more or less likely to be biologically meaningful than a statistically random mutation with uniform probability over the entire genome.  Based on Dembski’s work, if a hot spot repeatedly gives us biologically meaningful mutations more frequently than statistically random mutations over the whole genome, then this is evidence that the hot spot is part of a designed mechanism.

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December 30, 2008

Geology / Ian Juby’s Complete Creation Video Series

JB

Ian just finished posting his last video in his Complete Creation series (actually, there are more to come, but this was the last one which was part of his conference presentation).  The series is 18 videos long (approximately 9 hours), with more videos coming with additional explanatory information.

Anyway, the video series is fabulous.  I recommend you watch the whole thing.

Also, I have added Ian to our list of speakers.  If you need a speaker anywhere in the U.S. or Canada, Ian is probably heading your way sometime during the year.  Email speaking@bartlettpublishing.com to book a presentation with your Church or group.  Also be sure to check out Ian’s own website.

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December 11, 2008

Discussions around the Web / Todd’s New Blog and a New Book on Genesis

JB

Todd Wood, author of Understanding the Pattern of Life, and one of the BSG‘s founders, as well as part of the team which sequenced the rice genome, just started a new blog on Creation.  He has a great article summarizing Jean Lightner’s paper on skin color and the generation of diversity.

Also coming is a new book on Genesis and Creation edited by Terry Mortenson.  This books aims to be a seminary-level book for understanding the Creationist perspective on Genesis.  From the table of contents, it looks like it covers:

  • History of exegesis of Genesis
  • The events surrounding the Church’s change of position regarding Genesis
  • The relationship of nature to revelation
  • The genre of the text
  • Critiques of other interpretations
  • The relationship between Genesis and other near-eastern documents (this is actually not based on the table of contents but from a marketing announcement)

I hope to read it soon!

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